Professional Documents
Culture Documents
Chromosome analysis (karyotype) Normal male karyotype Donor has a well-known chromosome
variant with no clinical significance.
46,XY,inv(9)(p12q13) see attached.
Expanded Genetic Disease Carrier Variant Detected for Alpha- Partner testing recommended for HBB
Screening Panel attached- 502 diseases Thalassemia (HBA1/HBA2) before using this donor.
by gene sequencing. One copy of the alpha 3.7 duplication
(aaa/aa)
Personalized residual risk by gene is on
attached report. Negative for other genes sequenced
*No single test can screen for all genetic disorders. A negative screening result significantly reduces, but cannot eliminate, the
risk for these conditions in a pregnancy.
**Donor residual risk is the chance the donor is still a carrier after testing negative.
Positive Negative
Variant Detected for Alpha-Thalassemia (AR) Negative for all other genes tested
Associated gene(s): HBA1/HBA2 To view a full list of genes and diseases tested
Variant(s) Detected: One copy of the alpha 3.7 duplication please see Table 1 in this report
Recommendations
An alpha-thalassemia duplication allele is generally considered to be a benign polymorphism. Testing the partner for both alpha-
thalassemia and beta-thalassemia are recommended to assess the likelihood that the patients offspring may be affected with
thalassemia intermedia. Genetic counseling is recommended.
Please note that for female carriers of X-linked diseases, follow-up testing of a male partner is not indicated.
CGG repeat analysis of FMR1 for fragile X syndrome is not performed on males as repeat expansion of premutation alleles is not expected
in the male germline.
Individuals of Asian, African, Hispanic and Mediterranean ancestry should also be screened for hemoglobinopathies by CBC and
hemoglobin electrophoresis.
Consideration of residual risk by ethnicity after a negative carrier screen is recommended for the other diseases on the panel, especially
in the case of a positive family history for a specific disorder. Please note that residual risks for X-linked diseases (including full repeat
expansions for Fragile X syndrome) may not be accurate for males and the actual residual risk is likely to be lower.
than 4) can lead to a thalassaemia intermedia phenotype with a variable clinical presentation. No pathogenic or likely pathogenic variants were
identified by sequence analysis.
Typically, individuals have four functional alpha-globin genes: 2 copies of HBA1 and 2 copies of HBA2, whose expression is regulated by a cis-
acting regulatory element HS-40. Alpha-thalassemia carriers have three (silent carrier) or two (carrier of the alpha-thalassemia trait) functional
alpha-globin genes with or without a mild phenotype. Individuals with only one functional alpha-globin gene have HbH disease with
microcytic, hypochromic hemolytic anemia and hepatosplenomegaly. Loss of all four alpha-globin genes results in Hb Barts syndrome with
the accumulation of Hb Barts in red blood cells and hydrops fetalis, which is fatal in utero or shortly after birth.
Test description
This patient was tested for a panel of diseases using a combination of sequencing, targeted genotyping and copy number analysis. Please note
that negative results reduce but do not eliminate the possibility that this individual is a carrier for one or more of the disorders tested. Please see
Table 1 for a list of genes and diseases tested with the patient's personalized residual risk. If personalized residual risk is not provided, please
see the complete residual risk table at go.sema4.com/residualrisk. Only variants determined to be pathogenic or likely pathogenic are
reported in this carrier screening test.
Inheritance
Disease Gene Status Detailed Summary
Pattern
Positive
Negative
3-Phosphoglycerate Dehydrogenase Deficiency PHGDH AR Reduced Risk Personalized Residual Risk: 1 in 63,000
6-Pyruvoyl-Tetrahydropterin Synthase
PTS AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Deficiency
CD59-Mediated Hemolytic Anemia CD59 AR Reduced Risk Personalized Residual Risk: 1 in 415,000
Abetalipoproteinemia MTTP AR Reduced Risk Personalized Residual Risk: 1 in 3,200
Achalasia-Addisonianism-Alacrimia Syndrome AAAS AR Reduced Risk Personalized Residual Risk: 1 in 4,500
Achromatopsia (CNGA3 -Related) CNGA3 AR Reduced Risk Personalized Residual Risk: 1 in 830
Achromatopsia (CNGB3 -related) CNGB3 AR Reduced Risk Personalized Residual Risk: 1 in 8,600
Acute Infantile Liver Failure TRMU AR Reduced Risk Personalized Residual Risk: 1 in 9,400
Acyl-CoA Oxidase I Deficiency ACOX1 AR Reduced Risk Personalized Residual Risk: 1 in 39,000
Adams-Oliver Syndrome 4 EOGT AR Reduced Risk Personalized Residual Risk: 1 in 44,000
Adenosine Deaminase Deficiency ADA AR Reduced Risk Personalized Residual Risk: 1 in 5,100
Adrenocorticotropic Hormone Deficiency TBX19 AR Reduced Risk Personalized Residual Risk: 1 in 35,000
Aicardi-Goutieres Syndrome (TREX1-Related) TREX1 AR Reduced Risk Personalized Residual Risk: 1 in 3,200
Albinism, Oculocutaneous, Type III TYRP1 AR Reduced Risk Personalized Residual Risk: 1 in 3,500
Alport Syndrome (COL4A3 -Related) COL4A3 AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Alport Syndrome (COL4A4-Related) COL4A4 AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Alport Syndrome (COL4A5 -Related) COL4A5 XL Reduced Risk Personalized Residual Risk: 1 in 150,000
Antley-Bixler Syndrome (POR -Related) POR AR Reduced Risk Personalized Residual Risk: 1 in 4,000
Argininemia ARG1 AR Reduced Risk Personalized Residual Risk: 1 in 6,500
Ataxia With Isolated Vitamin E Deficiency TTPA AR Reduced Risk Personalized Residual Risk: 1 in 61,000
Bardet-Biedl Syndrome (BBS12 -Related) BBS12 AR Reduced Risk Personalized Residual Risk: 1 in 9,900
Bardet-Biedl Syndrome (BBS1-Related) BBS1 AR Reduced Risk Personalized Residual Risk: 1 in 6,400
Bardet-Biedl Syndrome (BBS2 -Related) BBS2 AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Bardet-Biedl Syndrome (BBS4-Related) BBS4 AR Reduced Risk Personalized Residual Risk: 1 in 22,000
Bare Lymphocyte Syndrome, Type II CIITA AR Reduced Risk Personalized Residual Risk: 1 in 35,000
Barth Syndrome TAZ XL Reduced Risk Personalized Residual Risk: 1 in 183,000
Bartter Syndrome, Type 3 CLCNKB AR Reduced Risk Personalized Residual Risk: 1 in 740
Bartter Syndrome, Type 4A BSND AR Reduced Risk Personalized Residual Risk: 1 in 91,000
Bernard-Soulier Syndrome, Type A1 GP1BA AR Reduced Risk Personalized Residual Risk: 1 in 42,000
Bernard-Soulier Syndrome, Type C GP9 AR Reduced Risk Personalized Residual Risk: 1 in 3,300
Bilateral Frontoparietal Polymicrogyria GPR56 AR Reduced Risk Personalized Residual Risk: 1 in 203,000
Carbamoylphosphate Synthetase I Deficiency CPS1 AR Reduced Risk Personalized Residual Risk: 1 in 1,100
Carnitine Acylcarnitine Translocase Deficiency SLC25A20 AR Reduced Risk Personalized Residual Risk: 1 in 4,100
Carnitine Palmitoyltransferase IA Deficiency CPT1A AR Reduced Risk Personalized Residual Risk: 1 in 24,000
Carnitine Palmitoyltransferase II Deficiency CPT2 AR Reduced Risk Personalized Residual Risk: 1 in 670
Cerebral Creatine Deficiency Syndrome 2 GAMT AR Reduced Risk Personalized Residual Risk: 1 in 2,100
Cerebral Creatine Deficiency Syndrome 3 GATM AR Reduced Risk Personalized Residual Risk: 1 in 7,900
Cerebral Dysgenesis, Neuropathy, Ichthyosis,
SNAP29 AR Reduced Risk Personalized Residual Risk: 1 in 1,730,000
and Palmoplantar Keratoderma Syndrome
Cerebrotendinous Xanthomatosis CYP27A1 AR Reduced Risk Personalized Residual Risk: 1 in 3,900
Charcot-Marie-Tooth Disease, Type 4D NDRG1 AR Reduced Risk Personalized Residual Risk: 1 in 730,000
Charcot-Marie-Tooth Disease, Type 5 / Arts
PRPS1 XL Reduced Risk Personalized Residual Risk: 1 in 114,000
Syndrome
Charcot-Marie-Tooth Disease, X-Linked GJB1 XL Reduced Risk Personalized Residual Risk: 1 in 11,000
Chronic Granulomatous Disease (CYBA-Related) CYBA AR Reduced Risk Personalized Residual Risk: 1 in 5,000
Chronic Granulomatous Disease (CYBB-Related) CYBB XL Reduced Risk Personalized Residual Risk: 1 in 294,000
Combined Factor V and VIII Deficiency LMAN1 AR Reduced Risk Personalized Residual Risk: 1 in 102,000
Combined Malonic and Methylmalonic Aciduria ACSF3 AR Reduced Risk Personalized Residual Risk: 1 in 2,400
Combined Oxidative Phosphorylation Deficiency
GFM1 AR Reduced Risk Personalized Residual Risk: 1 in 13,000
1
Combined Oxidative Phosphorylation Deficiency
TSFM AR Reduced Risk Personalized Residual Risk: 1 in 27,000
3
Combined Pituitary Hormone Deficiency 1 POU1F1 AR Reduced Risk Personalized Residual Risk: 1 in 3,900
Combined Pituitary Hormone Deficiency 2 PROP1 AR Reduced Risk Personalized Residual Risk: 1 in 2,800
Combined Pituitary Hormone Deficiency 3 LHX3 AR Reduced Risk Personalized Residual Risk: 1 in 140,000
Combined SAP Deficiency PSAP AR Reduced Risk Personalized Residual Risk: 1 in 44,000
Cone-Rod Dystrophy 6 / Leber Congenital
GUCY2D AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Amaurosis 1
Congenital Adrenal Hyperplasia due to 11-Beta-
CYP11B1 AR Reduced Risk Personalized Residual Risk: 1 in 520
Hydroxylase Deficiency
Congenital Adrenal Hyperplasia due to 17-
CYP17A1 AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Alpha-Hydroxylase Deficiency
CYP21A2 copy number: 2
CYP21A2 sequencing: Negative
Personalized Residual Risk (Congenital
Congenital Adrenal Hyperplasia due to 21- Adrenal Hyperplasia due to 21-Hydroxylase
CYP21A2 AR Reduced Risk
Hydroxylase Deficiency Deficiency (Non-Classic)): 1 in 200
Personalized Residual Risk (Congenital
Adrenal Hyperplasia due to 21-Hydroxylase
Deficiency (Classic)): 1 in 1,300
Congenital Adrenal Hypoplasia (NR0B1-Related) NR0B1 XL Reduced Risk Personalized Residual Risk: 1 in 353,000
Congenital Adrenal Insufficiency (CYP11A1-
CYP11A1 AR Reduced Risk Personalized Residual Risk: 1 in 6,100
Related)
Congenital Amegakaryocytic
MPL AR Reduced Risk Personalized Residual Risk: 1 in 3,100
Thrombocytopenia
Congenital Bile Acid Synthesis Defect (AKR1D1-
AKR1D1 AR Reduced Risk Personalized Residual Risk: 1 in 6,900
Related)
Congenital Bile Acid Synthesis Defect (HSD3B7 -
HSD3B7 AR Reduced Risk Personalized Residual Risk: 1 in 8,900
Related)
Congenital Disorder of Deglycosylation NGLY1 AR Reduced Risk Personalized Residual Risk: 1 in 14,000
Congenital Disorder of Glycosylation, Type Ia PMM2 AR Reduced Risk Personalized Residual Risk: 1 in 540
Congenital Disorder of Glycosylation, Type Ib MPI AR Reduced Risk Personalized Residual Risk: 1 in 5,600
Congenital Disorder of Glycosylation, Type Ic ALG6 AR Reduced Risk Personalized Residual Risk: 1 in 4,100
Congenital Disorder of Glycosylation, Type Im DOLK AR Reduced Risk Personalized Residual Risk: 1 in 134,000
Congenital Dyserythropoietic Anemia Type 2 SEC23B AR Reduced Risk Personalized Residual Risk: 1 in 1,000
Congenital Dyserythropoietic Anemia, Type Ia CDAN1 AR Reduced Risk Personalized Residual Risk: 1 in 470
Congenital Ichthyosis 4A and 4B ABCA12 AR Reduced Risk Personalized Residual Risk: 1 in 5,100
Congenital Insensitivity to Pain with Anhidrosis NTRK1 AR Reduced Risk Personalized Residual Risk: 1 in 5,700
Congenital Muscular Dystrophy (LAMA2 -
LAMA2 AR Reduced Risk Personalized Residual Risk: 1 in 640
Related)
Congenital Myasthenic Syndrome (CHAT-
CHAT AR Reduced Risk Personalized Residual Risk: 1 in 3,100
Related)
Congenital Myasthenic Syndrome (CHRNE-
CHRNE AR Reduced Risk Personalized Residual Risk: 1 in 4,100
Related)
Congenital Myasthenic Syndrome (DOK7 -
DOK7 AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Related)
Congenital Myasthenic Syndrome (RAPSN -
RAPSN AR Reduced Risk Personalized Residual Risk: 1 in 2,900
Related)
Congenital Neutropenia (HAX1-Related) HAX1 AR Reduced Risk Personalized Residual Risk: 1 in 82,000
Congenital Neutropenia (VPS45 -Related) VPS45 AR Reduced Risk Personalized Residual Risk: 1 in 163,000
Congenital Nongoitrous Hypothyroidism 1 TSHR AR Reduced Risk Personalized Residual Risk: 1 in 1,000
Congenital Nongoitrous Hypothyroidism 4 TSHB AR Reduced Risk Personalized Residual Risk: 1 in 118,000
Congenital Secretory Chloride Diarrhea 1 SLC26A3 AR Reduced Risk Personalized Residual Risk: 1 in 2,400
Corneal Dystrophy and Perceptive Deafness SLC4A11 AR Reduced Risk Personalized Residual Risk: 1 in 4,600
Corticosterone Methyloxidase Deficiency CYP11B2 AR Reduced Risk Personalized Residual Risk: 1 in 1,500
Cystic Fibrosis CFTR AR Reduced Risk Personalized Residual Risk: 1 in 440
Cystinosis CTNS AR Reduced Risk Personalized Residual Risk: 1 in 7,700
Cystinuria (SLC3A1-Related) SLC3A1 AR Reduced Risk Personalized Residual Risk: 1 in 590
Cytochrome C Oxidase Deficiency / Leigh
COX15 AR Reduced Risk Personalized Residual Risk: 1 in 3,300
Syndrome (COX15 -Related)
D-Bifunctional Protein Deficiency HSD17B4 AR Reduced Risk Personalized Residual Risk: 1 in 5,000
Deafness, Autosomal Recessive 3 MYO15A AR Reduced Risk Personalized Residual Risk: 1 in 240
Deafness, Autosomal Recessive 59 PJVK AR Reduced Risk Personalized Residual Risk: 1 in 3,700
Deafness, Autosomal Recessive 7 TMC1 AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Deafness, Autosomal Recessive 76 SYNE4 AR Reduced Risk Personalized Residual Risk: 1 in 43,000
Deafness, Autosomal Recessive 77 LOXHD1 AR Reduced Risk Personalized Residual Risk: 1 in 6,700
Deafness, Autosomal Recessive 8/10 TMPRSS3 AR Reduced Risk Personalized Residual Risk: 1 in 510
Deafness, Autosomal Recessive 9 OTOF AR Reduced Risk Personalized Residual Risk: 1 in 1,400
Dyskeratosis Congenita (RTEL1-Related) RTEL1 AR Reduced Risk Personalized Residual Risk: 1 in 9,800
Dystrophic Epidermolysis Bullosa COL7A1 AR Reduced Risk Personalized Residual Risk: 1 in 900
Ehlers-Danlos Syndrome, Type VI PLOD1 AR Reduced Risk Personalized Residual Risk: 1 in 20,000
Ehlers-Danlos Syndrome, Type VIIC ADAMTS2 AR Reduced Risk Personalized Residual Risk: 1 in 243,000
Ellis-Van Creveld Syndrome (EVC2 -Related) EVC2 AR Reduced Risk Personalized Residual Risk: 1 in 6,300
Ellis-van Creveld Syndrome (EVC-Related) EVC AR Reduced Risk Personalized Residual Risk: 1 in 4,200
Enhanced S-Cone Syndrome NR2E3 AR Reduced Risk Personalized Residual Risk: 1 in 1,600
Familial Hyperinsulinism (KCNJ11-Related) KCNJ11 AR Reduced Risk Personalized Residual Risk: 1 in 5,300
Familial Hyperphosphatemic Tumoral Calcinosis GALNT3 AR Reduced Risk Personalized Residual Risk: 1 in 7,800
Familial Mediterranean Fever MEFV AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Fanconi Anemia, Group A FANCA AR Reduced Risk Personalized Residual Risk: 1 in 1,100
Fanconi Anemia, Group C FANCC AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Fanconi Anemia, Group G FANCG AR Reduced Risk Personalized Residual Risk: 1 in 28,000
Fanconi-Bickel Syndrome SLC2A2 AR Reduced Risk Personalized Residual Risk: 1 in 4,000
FMR1 CGG repeat sizes: Not Performed
FMR1 Sequencing: Negative
Fragile X CGG triplet repeat expansion testing
Fragile X Syndrome FMR1 XL Reduced Risk was not performed at this time, as the patient
has either been previously tested or is a male.
Personalized Residual Risk: 1 in 19,000
Fructose-1,6-Bisphosphatase Deficiency FBP1 AR Reduced Risk Personalized Residual Risk: 1 in 2,600
Glanzmann Thrombasthenia (ITGA2B-Related) ITGA2B AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Glanzmann Thrombasthenia (ITGB3 -Related) ITGB3 AR Reduced Risk Personalized Residual Risk: 1 in 1,600
Glutaric Acidemia, Type I GCDH AR Reduced Risk Personalized Residual Risk: 1 in 2,700
Glutaric Acidemia, Type IIa ETFA AR Reduced Risk Personalized Residual Risk: 1 in 4,700
Glutaric Acidemia, Type IIb ETFB AR Reduced Risk Personalized Residual Risk: 1 in 5,900
Glutaric Acidemia, Type IIc ETFDH AR Reduced Risk Personalized Residual Risk: 1 in 1,700
Glutathione Synthetase Deficiency GSS AR Reduced Risk Personalized Residual Risk: 1 in 3,500
Glycine Encephalopathy (AMT-Related) AMT AR Reduced Risk Personalized Residual Risk: 1 in 5,700
Glycine Encephalopathy (GLDC-Related) GLDC AR Reduced Risk Personalized Residual Risk: 1 in 760
Glycogen Storage Disease, Type 0 GYS2 AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Glycogen Storage Disease, Type Ia G6PC AR Reduced Risk Personalized Residual Risk: 1 in 5,300
Glycogen Storage Disease, Type Ib SLC37A4 AR Reduced Risk Personalized Residual Risk: 1 in 7,300
Glycogen Storage Disease, Type II GAA AR Reduced Risk Personalized Residual Risk: 1 in 520
Glycogen Storage Disease, Type III AGL AR Reduced Risk Personalized Residual Risk: 1 in 5,600
Glycogen Storage Disease, Type V PYGM AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Glycogen Storage Disease, Type VI PYGL AR Reduced Risk Personalized Residual Risk: 1 in 1,600
Glycogen Storage Disease, Type VII PFKM AR Reduced Risk Personalized Residual Risk: 1 in 4,300
GRACILE Syndrome and Other BCS1L-Related
BCS1L AR Reduced Risk Personalized Residual Risk: 1 in 3,900
Disorders
Gray Platelet Syndrome NBEAL2 AR Reduced Risk Personalized Residual Risk: 1 in 6,800
Growth Hormone Deficiency, Type IB GHRHR AR Reduced Risk Personalized Residual Risk: 1 in 3,900
Hemochromatosis, Type 2A HFE2 AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Hereditary Spastic Paraparesis 49 TECPR2 AR Reduced Risk Personalized Residual Risk: 1 in 116,000
Hermansky-Pudlak Syndrome, Type 1 HPS1 AR Reduced Risk Personalized Residual Risk: 1 in 3,500
Hermansky-Pudlak Syndrome, Type 3 HPS3 AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Hermansky-Pudlak Syndrome, Type 4 HPS4 AR Reduced Risk Personalized Residual Risk: 1 in 35,000
Hermansky-Pudlak Syndrome, Type 6 HPS6 AR Reduced Risk Personalized Residual Risk: 1 in 87,000
HMG-CoA Lyase Deficiency HMGCL AR Reduced Risk Personalized Residual Risk: 1 in 2,700
Hmg-CoA Synthase 2 Deficiency HMGCS2 AR Reduced Risk Personalized Residual Risk: 1 in 2,000
Holocarboxylase Synthetase Deficiency HLCS AR Reduced Risk Personalized Residual Risk: 1 in 5,500
Homocystinuria (CBS-Related) CBS AR Reduced Risk Personalized Residual Risk: 1 in 1,400
Homocystinuria due to MTHFR Deficiency MTHFR AR Reduced Risk Personalized Residual Risk: 1 in 1,300
Homocystinuria, cblE Type MTRR AR Reduced Risk Personalized Residual Risk: 1 in 9,600
Homocystinuria-Megaloblastic Anemia,
MTR AR Reduced Risk Personalized Residual Risk: 1 in 2,100
Cobalamin G Type
Hydrocephalus L1CAM XL Reduced Risk Personalized Residual Risk: 1 in 40,000
Hydrolethalus Syndrome HYLS1 AR Reduced Risk Personalized Residual Risk: 1 in 52,000
Hyper-Igm Syndrome CD40LG XL Reduced Risk Personalized Residual Risk: 1 in 1,167,000
Hyperornithinemia-Hyperammonemia-
SLC25A15 AR Reduced Risk Personalized Residual Risk: 1 in 5,700
Homocitrullinuria Syndrome
Hyperuricemia, Pulmonary Hypertension, Renal
SARS2 AR Reduced Risk Personalized Residual Risk: 1 in 23,000
Failure, and Alkalosis
Hypohidrotic Ectodermal Dysplasia 1 EDA XL Reduced Risk Personalized Residual Risk: 1 in 22,000
Inclusion Body Myopathy 2 GNE AR Reduced Risk Personalized Residual Risk: 1 in 2,000
Infantile Cerebral and Cerebellar Atrophy MED17 AR Reduced Risk Personalized Residual Risk: 1 in 129,000
Infantile Neuroaxonal Dystrophy 1 and other
PLA2G6 AR Reduced Risk Personalized Residual Risk: 1 in 690
PLA2G6-Related Disorders
Intellectual Disability, Autosomal Recessive 3 CC2D1A AR Reduced Risk Personalized Residual Risk: 1 in 220,000
Lamellar Ichthyosis, Type 1 TGM1 AR Reduced Risk Personalized Residual Risk: 1 in 1,500
Limb-Girdle Muscular Dystrophy, Type 2C SGCG AR Reduced Risk Personalized Residual Risk: 1 in 4,900
Limb-Girdle Muscular Dystrophy, Type 2D SGCA AR Reduced Risk Personalized Residual Risk: 1 in 3,500
Limb-Girdle Muscular Dystrophy, Type 2E SGCB AR Reduced Risk Personalized Residual Risk: 1 in 31,000
Limb-Girdle Muscular Dystrophy, Type 2F SGCD AR Reduced Risk Personalized Residual Risk: 1 in 52,000
Limb-Girdle Muscular Dystrophy, Type 2H TRIM32 AR Reduced Risk Personalized Residual Risk: 1 in 10,000
Limb-Girdle Muscular Dystrophy, Type 2I FKRP AR Reduced Risk Personalized Residual Risk: 1 in 1,400
Limb-Girdle Muscular Dystrophy, Type 2L ANO5 AR Reduced Risk Personalized Residual Risk: 1 in 660
Lipoamide Dehydrogenase Deficiency DLD AR Reduced Risk Personalized Residual Risk: 1 in 14,000
Lipoid Adrenal Hyperplasia STAR AR Reduced Risk Personalized Residual Risk: 1 in 3,600
Lipoprotein Lipase Deficiency LPL AR Reduced Risk Personalized Residual Risk: 1 in 2,400
Long-Chain 3-Hydroxyacyl-CoA Dehydrogenase
HADHA AR Reduced Risk Personalized Residual Risk: 1 in 5,900
Deficiency
Lowe Syndrome OCRL XL Reduced Risk Personalized Residual Risk: 1 in 1,375,000
Lysinuric Protein Intolerance SLC7A7 AR Reduced Risk Personalized Residual Risk: 1 in 3,000
Malonyl-CoA Decarboxylase Deficiency MLYCD AR Reduced Risk Personalized Residual Risk: 1 in 2,800
Maple Syrup Urine Disease, Type 1a BCKDHA AR Reduced Risk Personalized Residual Risk: 1 in 5,100
Maple Syrup Urine Disease, Type 1b BCKDHB AR Reduced Risk Personalized Residual Risk: 1 in 1,100
Maple Syrup Urine Disease, Type 2 DBT AR Reduced Risk Personalized Residual Risk: 1 in 3,600
Meckel Syndrome 1 / Bardet-Biedl Syndrome 13 MKS1 AR Reduced Risk Personalized Residual Risk: 1 in 1,700
Medium Chain Acyl-CoA Dehydrogenase
ACADM AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Deficiency
MEDNIK Syndrome AP1S1 AR Reduced Risk Personalized Residual Risk: 1 in 211,000
Megalencephalic Leukoencephalopathy with
MLC1 AR Reduced Risk Personalized Residual Risk: 1 in 4,300
Subcortical Cysts
Megaloblastic Anemia 1 AMN AR Reduced Risk Personalized Residual Risk: 1 in 6,300
Methylmalonic Acidemia (MMAB-Related) MMAB AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Methylmalonic Acidemia (MUT-Related) MUT AR Reduced Risk Personalized Residual Risk: 1 in 1,300
Methylmalonic Aciduria and Homocystinuria,
MMACHC AR Reduced Risk Personalized Residual Risk: 1 in 6,800
Cobalamin C Type
Methylmalonic Aciduria and Homocystinuria,
MMADHC AR Reduced Risk Personalized Residual Risk: 1 in 219,000
Cobalamin D Type
Methylmalonic Aciduria and Homocystinuria,
LMBRD1 AR Reduced Risk Personalized Residual Risk: 1 in 6,600
Cobalamin F Type
Methylmalonyl-CoA Epimerase Deficiency MCEE AR Reduced Risk Personalized Residual Risk: 1 in 98,000
Mitochondrial DNA Depletion Syndrome 3 DGUOK AR Reduced Risk Personalized Residual Risk: 1 in 5,200
Mitochondrial DNA Depletion Syndrome 4A and
POLG AR Reduced Risk Personalized Residual Risk: 1 in 320
4B and other POLG-Related Disorders
Mitochondrial DNA Depletion Syndrome 5 SUCLA2 AR Reduced Risk Personalized Residual Risk: 1 in 78,000
Mitochondrial DNA Depletion Syndrome 6 /
MPV17 AR Reduced Risk Personalized Residual Risk: 1 in 4,400
Navajo Neurohepatopathy
Mucopolysaccharidosis Type IIIB NAGLU AR Reduced Risk Personalized Residual Risk: 1 in 950
Mucopolysaccharidosis Type IIIC HGSNAT AR Reduced Risk Personalized Residual Risk: 1 in 3,200
Mucopolysaccharidosis Type IIID GNS AR Reduced Risk Personalized Residual Risk: 1 in 137,000
Mucopolysaccharidosis Type IVa GALNS AR Reduced Risk Personalized Residual Risk: 1 in 690
Mucopolysaccharidosis Type IVb / GM1
GLB1 AR Reduced Risk Personalized Residual Risk: 1 in 1,700
Gangliosidosis
Mucopolysaccharidosis type IX HYAL1 AR Reduced Risk Personalized Residual Risk: 1 in 149,000
Mucopolysaccharidosis type VI ARSB AR Reduced Risk Personalized Residual Risk: 1 in 1,300
Neuronal Ceroid-Lipofuscinosis (CLN5 -Related) CLN5 AR Reduced Risk Personalized Residual Risk: 1 in 4,300
Neuronal Ceroid-Lipofuscinosis (CLN6-Related) CLN6 AR Reduced Risk Personalized Residual Risk: 1 in 8,600
Neuronal Ceroid-Lipofuscinosis (CLN8-Related) CLN8 AR Reduced Risk Personalized Residual Risk: 1 in 3,100
Neuronal Ceroid-Lipofuscinosis (MFSD8-
MFSD8 AR Reduced Risk Personalized Residual Risk: 1 in 6,200
Related)
Neuronal Ceroid-Lipofuscinosis (PPT1-Related) PPT1 AR Reduced Risk Personalized Residual Risk: 1 in 7,500
Neuronal Ceroid-Lipofuscinosis (TPP1-Related) TPP1 AR Reduced Risk Personalized Residual Risk: 1 in 6,300
Niemann-Pick Disease (SMPD1-Related) SMPD1 AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Niemann-Pick Disease, Type C (NPC1-Related) NPC1 AR Reduced Risk Personalized Residual Risk: 1 in 690
Niemann-Pick Disease, Type C (NPC2 -Related) NPC2 AR Reduced Risk Personalized Residual Risk: 1 in 6,600
Nijmegen Breakage Syndrome NBN AR Reduced Risk Personalized Residual Risk: 1 in 14,000
Non-Syndromic Hearing Loss (GJB2 -Related) GJB2 AR Reduced Risk Personalized Residual Risk: 1 in 600
Oculocutaneous Albinism, Type IA / IB TYR AR Reduced Risk Personalized Residual Risk: 1 in 240
Oculocutaneous Albinism, Type IV SLC45A2 AR Reduced Risk Personalized Residual Risk: 1 in 830
Odonto-Onycho-Dermal Dysplasia / Schopf-
WNT10A AR Reduced Risk Personalized Residual Risk: 1 in 1,900
Schulz-Passarge Syndrome
Omenn Syndrome (RAG2 -Related) RAG2 AR Reduced Risk Personalized Residual Risk: 1 in 17,000
Omenn Syndrome / Severe Combined
DCLRE1C AR Reduced Risk Personalized Residual Risk: 1 in 5,500
Immunodeficiency, Athabaskan-Type
Omenn Syndrome and other RAG1-Related
RAG1 AR Reduced Risk Personalized Residual Risk: 1 in 850
Disorders
Ornithine Aminotransferase Deficiency OAT AR Reduced Risk Personalized Residual Risk: 1 in 6,400
Ornithine Transcarbamylase Deficiency OTC XL Reduced Risk Personalized Residual Risk: 1 in 103,000
Osteogenesis Imperfecta, Type XI FKBP10 AR Reduced Risk Personalized Residual Risk: 1 in 9,500
Peroxisome Biogenesis Disorder 7A and 7B PEX26 AR Reduced Risk Personalized Residual Risk: 1 in 70,000
Phenylalanine Hydroxylase Deficiency PAH AR Reduced Risk Personalized Residual Risk: 1 in 340
Polycystic Kidney Disease, Autosomal
PKHD1 AR Reduced Risk Personalized Residual Risk: 1 in 450
Recessive
Polyglandular Autoimmune Syndrome, Type 1 AIRE AR Reduced Risk Personalized Residual Risk: 1 in 5,300
Pontocerebellar Hypoplasia, Type 1A VRK1 AR Reduced Risk Personalized Residual Risk: 1 in 25,000
Pontocerebellar Hypoplasia, Type 1B EXOSC3 AR Reduced Risk Personalized Residual Risk: 1 in 10,000
Pontocerebellar Hypoplasia, Type 2A and Type 4 TSEN54 AR Reduced Risk Personalized Residual Risk: 1 in 4,700
Pontocerebellar Hypoplasia, Type 2E VPS53 AR Reduced Risk Personalized Residual Risk: 1 in 139,000
Pontocerebellar Hypoplasia, Type 6 RARS2 AR Reduced Risk Personalized Residual Risk: 1 in 8,600
Primary Carnitine Deficiency SLC22A5 AR Reduced Risk Personalized Residual Risk: 1 in 1,500
Primary Ciliary Dyskinesia (CCDC103 -Related) CCDC103 AR Reduced Risk Personalized Residual Risk: 1 in 27,000
Primary Ciliary Dyskinesia (CCDC151-Related) CCDC151 AR Reduced Risk Personalized Residual Risk: 1 in 59,000
Primary Ciliary Dyskinesia (CCDC39-Related) CCDC39 AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Primary Ciliary Dyskinesia (DNAH5 -Related) DNAH5 AR Reduced Risk Personalized Residual Risk: 1 in 1,500
Primary Ciliary Dyskinesia (DNAI1-Related) DNAI1 AR Reduced Risk Personalized Residual Risk: 1 in 5,000
Primary Ciliary Dyskinesia (DNAI2 -Related) DNAI2 AR Reduced Risk Personalized Residual Risk: 1 in 76,000
Primary Ciliary Dyskinesia (RSPH9-Related) RSPH9 AR Reduced Risk Personalized Residual Risk: 1 in 253,000
Primary Coenzyme Q10 Deficiency 7 COQ4 AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Primary Congenital Glaucoma 3A CYP1B1 AR Reduced Risk Personalized Residual Risk: 1 in 880
Primary Hyperoxaluria, Type 1 AGXT AR Reduced Risk Personalized Residual Risk: 1 in 1,900
Primary Hyperoxaluria, Type 2 GRHPR AR Reduced Risk Personalized Residual Risk: 1 in 11,000
Primary Hyperoxaluria, Type 3 HOGA1 AR Reduced Risk Personalized Residual Risk: 1 in 2,400
Progressive Cerebello-Cerebral Atrophy SEPSECS AR Reduced Risk Personalized Residual Risk: 1 in 6,400
Progressive Familial Intrahepatic Cholestasis,
ABCB11 AR Reduced Risk Personalized Residual Risk: 1 in 950
Type 2
Progressive Myoclonic Epilepsy, Type 1B PRICKLE1 AR Reduced Risk Personalized Residual Risk: 1 in 98,000
Progressive Pseudorheumatoid Dysplasia WISP3 AR Reduced Risk Personalized Residual Risk: 1 in 5,600
Propionic Acidemia (PCCA-Related) PCCA AR Reduced Risk Personalized Residual Risk: 1 in 2,600
Propionic Acidemia (PCCB-Related) PCCB AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Pulmonary Surfactant Dysfunction ABCA3 AR Reduced Risk Personalized Residual Risk: 1 in 1,200
Pyridoxamine 5'-Phosphate Oxidase Deficiency PNPO AR Reduced Risk Personalized Residual Risk: 1 in 10,000
Pyruvate Dehydrogenase E1-Alpha Deficiency PDHA1 XL Reduced Risk Personalized Residual Risk: 1 in 139,000
Pyruvate Dehydrogenase E1-Beta Deficiency PDHB AR Reduced Risk Personalized Residual Risk: 1 in 15,000
Renal Tubular Acidosis and Deafness ATP6V1B1 AR Reduced Risk Personalized Residual Risk: 1 in 6,600
Retinitis Pigmentosa 25 EYS AR Reduced Risk Personalized Residual Risk: 1 in 1,800
Rhizomelic Chondrodysplasia Punctata, Type 1 PEX7 AR Reduced Risk Personalized Residual Risk: 1 in 10,000
Rhizomelic Chondrodysplasia Punctata, Type 3 AGPS AR Reduced Risk Personalized Residual Risk: 1 in 620,000
Schimke Immunoosseous Dysplasia SMARCAL1 AR Reduced Risk Personalized Residual Risk: 1 in 3,800
Seckel Syndrome 5 / Microcephaly 9 CEP152 AR Reduced Risk Personalized Residual Risk: 1 in 1,700
Severe Neonatal Hyperparathyroidism CASR AR Reduced Risk Personalized Residual Risk: 1 in 2,700
Short Stature, Onychodysplasia, Facial
POC1A AR Reduced Risk Personalized Residual Risk: 1 in 108,000
Dysmorphism, and Hypotrichosis
Short-Chain Acyl-CoA Dehydrogenase
ACADS AR Reduced Risk Personalized Residual Risk: 1 in 660
Deficiency
Shwachman-Diamond Syndrome SBDS AR Reduced Risk Personalized Residual Risk: 1 in 1,700
Sialidosis, Type I and Type II NEU1 AR Reduced Risk Personalized Residual Risk: 1 in 2,000
Tyrosinemia, Type III HPD AR Reduced Risk Personalized Residual Risk: 1 in 266,000
Usher Syndrome, Type IB MYO7A AR Reduced Risk Personalized Residual Risk: 1 in 1,000
Usher Syndrome, Type IC USH1C AR Reduced Risk Personalized Residual Risk: 1 in 1,600
Usher Syndrome, Type ID CDH23 AR Reduced Risk Personalized Residual Risk: 1 in 1,400
Usher Syndrome, Type IF PCDH15 AR Reduced Risk Personalized Residual Risk: 1 in 3,800
Usher Syndrome, Type IIA USH2A AR Reduced Risk Personalized Residual Risk: 1 in 290
Usher Syndrome, Type III CLRN1 AR Reduced Risk Personalized Residual Risk: 1 in 1,300
Very Long Chain Acyl-CoA Dehydrogenase
ACADVL AR Reduced Risk Personalized Residual Risk: 1 in 920
Deficiency
Vitamin D-Dependent Rickets, Type I CYP27B1 AR Reduced Risk Personalized Residual Risk: 1 in 7,900
Vitamin D-Resistant Rickets, Type IIA VDR AR Reduced Risk Personalized Residual Risk: 1 in 17,000
Walker-Warburg Syndrome and Other FKTN -
FKTN AR Reduced Risk Personalized Residual Risk: 1 in 4,200
Related Dystrophies
Werner Syndrome WRN AR Reduced Risk Personalized Residual Risk: 1 in 9,200
Wiskott-Aldrich Syndrome (WAS-Related) WAS XL Reduced Risk Personalized Residual Risk: 1 in 1,203,000
Wolcott-Rallison Syndrome EIF2AK3 AR Reduced Risk Personalized Residual Risk: 1 in 22,000
Wolman Disease / Cholesteryl Ester Storage
LIPA AR Reduced Risk Personalized Residual Risk: 1 in 3,200
Disease
Woodhouse-Sakati Syndrome DCAF17 AR Reduced Risk Personalized Residual Risk: 1 in 81,000
X-Linked Juvenile Retinoschisis RS1 XL Reduced Risk Personalized Residual Risk: 1 in 40,000
X-Linked Severe Combined Immunodeficiency IL2RG XL Reduced Risk Personalized Residual Risk: 1 in 250,000
Xeroderma Pigmentosum (POLH-Related) POLH AR Reduced Risk Personalized Residual Risk: 1 in 5,900
Xeroderma Pigmentosum, Group A XPA AR Reduced Risk Personalized Residual Risk: 1 in 11,000
Xeroderma Pigmentosum, Group C XPC AR Reduced Risk Personalized Residual Risk: 1 in 12,000
Xeroderma Pigmentosum, Group G ERCC5 AR Reduced Risk Personalized Residual Risk: 1 in 3,000
Zellweger Syndrome Spectrum (PEX10-Related) PEX10 AR Reduced Risk Personalized Residual Risk: 1 in 6,300
Zellweger Syndrome Spectrum (PEX1-Related) PEX1 AR Reduced Risk Personalized Residual Risk: 1 in 2,000
Zellweger Syndrome Spectrum (PEX2 -Related) PEX2 AR Reduced Risk Personalized Residual Risk: 1 in 77,000
Zellweger Syndrome Spectrum (PEX6-Related) PEX6 AR Reduced Risk Personalized Residual Risk: 1 in 1,600
PCR amplification using Asuragen, Inc. AmplideX ®FMR1 PCR reagents followed by capillary electrophoresis for allele sizing was performed.
Samples positive for FMR1 CGG repeats in the premutation and full mutation size range were further analyzed by Southern blot analysis to
assess the size and methylation status of the FMR1 CGG repeat.
Genotyping (Analytical Detection Rate >99%)
Multiplex PCR amplification and allele specific primer extension analyses using the MassARRAY® System were used to identify certain
recurrent variants that are complex in nature or are present in low copy repeats. Rare sequence variants may interfere with assay performance.
Multiplex Ligation-Dependent Probe Amplification (MLPA) (Analytical Detection Rate >99%)
MLPA® probe sets and reagents from MRC-Holland were used for copy number analysis of specific targets versus known control samples.
False positive or negative results may occur due to rare sequence variants in target regions detected by MLPA probes. Analytical sensitivity and
specificity of the MLPA method are both 99%.
For alpha thalassemia, the copy numbers of the HBA1 and HBA2 genes were analyzed. Alpha-globin gene deletions, triplications, and the
Constant Spring (CS) mutation are assessed. This test is expected to detect approximately 90% of all alpha-thalassemia mutations, varying by
ethnicity. carriers of alpha-thalassemia with three or more HBA copies on one chromosome, and one or no copies on the other chromosome,
may not be detected. With the exception of triplications, other benign alpha-globin gene polymorphisms will not be reported. Analyses of HBA1
and HBA2 are performed in association with long-range PCR of the coding regions followed by short-read sequencing.
For Duchenne muscular dystrophy, the copy numbers of all DMD exons were analyzed. Potentially pathogenic single exon deletions and
duplications are confirmed by a second method. Analysis of DMD is performed in association with sequencing of the coding regions.
For congenital adrenal hyperplasia, the copy number of the CYP21A2 gene was analyzed. This analysis can detect large deletions typically due
to unequal meiotic crossing-over between CYP21A2 and the pseudogene CYP21A1P. Classic 30-kb deletions make up approximately 20% of
CYP21A2 pathogenic alleles. This test may also identify certain point mutations in CYP21A2 caused by gene conversion events between
CYP21A2 and CYP21A1P. Some carriers may not be identified by dosage sensitive methods as this testing cannot detect individuals with two
copies (duplication) of the CYP21A2 gene on one chromosome and loss of CYP21A2 (deletion) on the other chromosome. Analysis of CYP21A2 is
performed in association with long-range PCR of the coding regions followed by short-read sequencing.
For spinal muscular atrophy (SMA), the copy numbers of the SMN1 and SMN2 genes were analyzed. The individual dosage of exons 7 and 8 as
well as the combined dosage of exons 1, 4, 6 and 8 of SMN1 and SMN2 were assessed. Copy number gains and losses can be detected with
this assay. Depending on ethnicity, 6 - 29 % of carriers will not be identified by dosage sensitive methods as this testing cannot detect
individuals with two copies (duplication) of the SMN1 gene on one chromosome and loss of SMN1 (deletion) on the other chromosome (silent
2+0 carrier) or individuals that carry an intragenic mutation in SMN1. Please also note that 2% of individuals diagnosed with SMA have a
causative SMN1 variant that occurred de novo, and therefore cannot be picked up by carrier screening in the parents. Analysis of SMN1 is
performed in association with short-read sequencing of exons 2a-7, followed by confirmation using long-range PCR (described below).
The presence of the c.*3+80T>G (chr5:70,247,901T>G) variant allele in an individual with Ashkenazi Jewish or Asian ancestry is typically
indicative of a duplication of SMN1. When present in an Ashkenazi Jewish or Asian individual with two copies of SMN1, c.*3+80T>G is likely
indicative of a silent (2+0) carrier. In individuals with two copies of SMN1 with African American, Hispanic or Caucasian ancestry, the presence
or absence of c.*3+80T>G significantly increases or decreases, respectively, the likelihood of being a silent 2+0 silent carrier.
MLPA for Gaucher disease (GBA), cystic fibrosis (CFTR), and non-syndromic hearing loss (GJB2/GJB6) will only be performed if indicated for
confirmation of detected CNVs. If GBA analysis was performed, the copy numbers of exons 1, 3, 4, and 6 - 10 of the GBA gene (of 11 exons total)
were analyzed. If CFTR analysis was performed, the copy numbers of all 27 CFTR exons were analyzed. If GJB2/GJB6 analysis was performed,
the copy number of the two GJB2 exons were analyzed, as well as the presence or absence of the two upstream deletions of the GJB2
regulatory region, del(GJB6-D13S1830) and del(GJB6-D13S1854).
Next Generation Sequencing (NGS) (Analytical Detection Rate >95%)
NGS was performed on a panel of genes for the purpose of identifying pathogenic or likely pathogenic variants.
Agilent SureSelectTMXT Low Input technology was used with a custom capture library to target the exonic regions and intron/exon splice
junctions of the relevant genes, as well as a number of UTR, intronic or promoter regions that contain previously reported mutations. Libraries
were pooled and sequenced on the Illumina NovaSeq 9000 platform, using paired-end 100 bp reads. The sequencing data was analyzed using
a custom bioinformatics algorithm designed and validated in house.
The coding exons and splice junctions of the known protein-coding RefSeq genes were assessed for the average depth of coverage (minimum
of 20X) and data quality threshold values. Most exons not meeting a minimum of >20X read depth across the exon are further analyzed by
Sanger sequencing. Please note that several genomic regions present difficulties in mapping or obtaining read depth >20X. These regions,
which are described below, will not be reflexed to Sanger sequencing if the mapping quality or coverage is poor. Any variants identified during
testing in these regions are confirmed by a second method and reported if determined to be pathogenic or likely pathogenic. However, as there
is a possibility of false negative results within these regions, detection rates and residual risks for these genes have been calculated with the
presumption that variants in these exons will not be detected, unless included in the MassARRAY® genotyping platform.
Exceptions: ABCD1 (NM_000033.3) exons 8 and 9; ACADSB (NM_ 001609.3) chr10:124,810,695-124,810,707 (partial exon 9); ADA (NM_000022.2)
exon 1; ADAMTS2 (NM_014244.4) exon 1; AGPS (NM_003659.3) chr2:178,257,512-178,257,649 (partial exon 1); ALDH7A1 (NM_001182.4)
chr5:125,911,150-125,911,163 (partial exon 7) and chr5:125,896,807-125,896,821 (partial exon 10); ALMS1 (NM_015120.4) chr2:73,612,990-73,613,041
(partial exon 1); APOPT1 (NM_ 032374.4) chr14:104,040,437-104,040,455 (partial exon 3); CDAN1 (NM_138477.2) exon 2; CEP152 (NM_014985.3)
chr15:49,061,146-49,061,165 (partial exon 14) and exon 22; CEP290 (NM_025114.3) exon 5, exon 7, chr12:88,519,017-88,519,039 (partial exon 13),
chr12:88,514,049-88,514,058 (partial exon 15), chr12:88,502,837-88,502,841 (partial exon 23), chr12:88,481,551-88,481,589 (partial exon 32),
chr12:88,471,605-88,471,700 (partial exon 40); CFTR (NM_000492.3) exon 10; COL4A4 (NM_000092.4) chr2:227,942,604-227,942,619 (partial exon
25); COX10 (NM_001303.3) exon 6; CYP11B1 (NM_000497.3) exons 3-7; CYP11B2 (NM_000498.3) exons 3-7; DNAI2 (NM_023036.4) chr17:72,308,136-
72,308,147 (partial exon 12); DOK7 (NM_173660.4) chr4:3,465,131-3,465,161 (partial exon 1) and exon 2; DUOX2 (NM_014080.4) exons 6-8; EIF2AK3
(NM_004836.5 exon 8; EVC (NM_153717.2) exon 1; FH (NM_000143.3) exon 1; GAMT (NM_000156.5 exon 1; GLDC (NM_000170.2) exon 1; GNPTAB
(NM_024312.4) chr17:4,837,000-4,837,400 (partial exon 2); GNPTG (NM_032520.4) exon 1; GHR (NM_000163.4) exon 3; GYS2 (NM_021957.3)
chr12:21,699,370-21,699,409 (partial exon 12); HGSNAT (NM_152419.2) exon 1; IDS (NM_000202.6 exon 3; ITGB4 (NM_000213.4) chr17:73,749,976-
73,750,060 (partial exon 33); JAK3 (NM_000215.3) chr19:17,950,462-17,950,483 (partial exon 10); LIFR (NM_002310.5 exon 19; LMBRD1
(NM_018368.3) chr6:70,459,226-70,459,257 (partial exon 5), chr6:70,447,828-70,447,836 (partial exon 7) and exon 12; LYST (NM_000081.3)
chr1:235,944,158-235,944,176 (partial exon 16) and chr1:235,875,350-235,875,362 (partial exon 43); MLYCD (NM_012213.2) chr16:83,933,242-
83,933,282 (partial exon 1); MTR (NM_000254.2) chr1 237,024,418-237,024,439 (partial exon 20) and chr1:237,038,019-237,038,029 (partial exon 24);
NBEAL2 (NM_015175.2) chr3 47,021,385-47,021,407 (partial exon 1); NEB (NM_001271208.1 exons 82-105; NPC1 (NM_000271.4) chr18:21,123,519-
21,123,538 (partial exon 14); NPHP1 (NM_000272.3) chr2:110,937,251-110,937,263 (partial exon 3); OCRL (NM_000276.3) chrX:128,674,450-128,674,460
(partial exon 1); PHKB (NM_000293.2) exon 1 and chr16:47,732,498-47,732,504 (partial exon 30); PIGN (NM_176787.4) chr18:59,815,547-59,815,576
(partial exon 8); PIP5K1C (NM_012398.2) exon 1 and chr19:3637602-3637616 (partial exon 17); POU1F1 (NM_000306.3) exon 5; PTPRC (NM_002838.4)
exons 11 and 23; PUS1 (NM_025215.5 chr12:132,414,446-132,414,532 (partial exon 2); RPGRIP1L (NM_015272.2) exon 23; SGSH (NM_000199.3)
chr17:78,194,022-78,194,072 (partial exon 1); SLC6A8 (NM_005629.3) exons 3 and 4; ST3GAL5 (NM_003896.3) exon 1; SURF1 (NM_003172.3)
chr9:136,223,269-136,223,307 (partial exon 1); TRPM6 (NM_017662.4) chr9:77,362,800-77,362,811 (partial exon 31); TSEN54 (NM_207346.2) exon 1; TYR
(NM_000372.4) exon 5; VWF (NM_000552.3) exons 24-26, chr12:6,125,675-6,125,684 (partial exon 30), chr12:6,121,244-6,121,265 (partial exon 33),
and exon 34.
This test will detect variants within the exons and the intron-exon boundaries of the target regions. Variants outside these regions may not be
detected, including, but not limited to, UTRs, promoters, and deep intronic areas, or regions that fall into the Exceptions mentioned above. This
technology may not detect all small insertion/deletions and is not diagnostic for repeat expansions and structural genomic variation. In
addition, a mutation(s) in a gene not included on the panel could be present in this patient.
Variant interpretation and classification was performed based on the American College of Medical Genetics Standards and Guidelines for the
Interpretation of Sequence Variants (Richards et al, 2015). All potentially pathogenic variants may be confirmed by either a specific genotyping
assay or Sanger sequencing, if indicated. Any benign variants, likely benign variants or variants of uncertain significance identified during this
analysis will not be reported.
Agilent SureSelectTMXT Low-Input technology was utilized in order to create whole-genome libraries for each patient sample. Libraries were
then pooled and sequenced on the Illumina NovaSeq platform. Each sequencing lane was multiplexed to achieve 0.4-2x genome coverage,
using paired-end 100 bp reads. The sequencing data underwent ancestral analysis using a customized, licensed bioinformatics algorithm that
was validated in house. Identified sub-ethnic groupings were binned into one of 7 continental-level groups (African, East Asian, South Asian,
Non-Finnish European, Finnish, Native American, and Ashkenazi Jewish) or, for those ethnicities that matched poorly to the continental-level
groups, an 8th “unassigned” group, which were then used to select residual risk values for each gene. For individuals belonging to multiple high-
level ethnic groupings, a weighting strategy was used to select the most appropriate residual risk. For genes that had insufficient data to
calculate ethnic-specific residual risk values, or for sub-ethnic groupings that fell into the “unassigned” group, a “worldwide” residual risk was
used. This “worldwide” residual risk was calculated using data from all available continental-level groups.
Sanger Sequencing (Confirmation method) (Accuracy >99%)
Sanger sequencing, as indicated, was performed using BigDye Terminator chemistry with the ABI 3730 DNA analyzer with target specific
amplicons. It also may be used to supplement specific guaranteed target regions that fail NGS sequencing due to poor quality or low depth of
coverage (<20 reads) or as a confirmatory method for NGS positive results. False negative results may occur if rare variants interfere with
amplification or annealing.
Tay-Sachs Disease (TSD) Enzyme Analysis (Analytical Detection Rate >98%)
Hexosaminidase activity and Hex A% activity were measured by a standard heat-inactivation, fluorometric method using artificial 4-MU-β-N-
acetyl glucosaminide (4-MUG) substrate. This assay is highly sensitive and accurate in detecting Tay-Sachs carriers and individuals affected
with TSD. Normal ranges of Hex A% activity are 55.0-72.0 for white blood cells and 58.0-72.0 for plasma. It is estimated that less than 0.5% of
Tay-Sachs carriers have non-carrier levels of percent Hex A activity, and therefore may not be identified by this assay. In addition, this assay
may detect individuals that are carriers of or are affected with Sandhoff disease. False positive results may occur if benign variants, such as
pseudodeficiency alleles, interfere with the enzymatic assay. False negative results may occur if both HEXA and HEXB pathogenic or
pseudodeficiency variants are present in the same individual.
Please note these tests were developed and their performance characteristics were determined by Sema4 Opco, Inc. They have not been
cleared or approved by the FDA. These analyses generally provide highly accurate information regarding the patient's carrier or affected status.
Despite this high level of accuracy, it should be kept in mind that there are many potential sources of diagnostic error, including
misidentification of samples, polymorphisms, or other rare genetic variants that interfere with analysis. Families should understand that rare
diagnostic errors may occur for these reasons.
SELECTED REFERENCES
Carrier Screening
Grody W et al. ACMG position statement on prenatal/preconception expanded carrier screening. Genet Med. 2013 15:482-3.
Fragile X syndrome:
Chen L et al. An information-rich CGG repeat primed PCR that detects the full range of Fragile X expanded alleles and minimizes the need for
Southern blot analysis. J Mol Diag 2010 12:589-600.
Spinal Muscular Atrophy:
Luo M et al. An Ashkenazi Jewish SMN1 haplotype specific to duplication alleles improves pan-ethnic carrier screening for spinal muscular
atrophy. Genet Med. 2014 16:149-56.
Ashkenazi Jewish Disorders:
Scott SA et al. Experience with carrier screening and prenatal diagnosis for sixteen Ashkenazi Jewish Genetic Diseases. Hum. Mutat. 2010 31:1-
11.
Duchenne Muscular Dystrophy:
Flanigan KM et al. Mutational spectrum of DMD mutations in dystrophinopathy patients: application of modern diagnostic techniques to a large
cohort. Hum Mutat. 2009 30:1657-66.
Variant Classification:
Richards S et al. Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American
College of Medical Genetics and Genomics and the Association for Molecular Pathology. Genet Med. 2015 May;17(5):405-24
Additional disease-specific references available upon request.
Ward: FFAXCB
Cytogenetic Report
CHROMOSOME ANALYSIS, BLOOD - 14596 Lab:EZ
CHROMOSOME ANALYSIS, BLOOD
Order ID:
Specimen Type: Blood
Clinical Indication: Encounter of male for testing for
disease carrier status for procrea management.
RESULT:
NORMAL MALE KARYOTYPE
INTERPRETATION:
Chromosome analysis revealed normal G-band patterns within the limits of standard cytogenetic analysis.
The inv(9)(p12q13) seen in all metaphase cells is a well-known chromosomal variant with no clinical
significance.
Please expect the results of any other concurrent study in a separate report.
NOMENCLATURE:
46,XY,inv(9)(p12q13)
ASSAY INFORMATION:
This test does not address genetic disorders that cannot be detected by standard cytogenetic methods or rare
events such as low level mosaicism or subtle rearrangements.
PERFORMING SITE:
EZ QUEST DIAGNOSTICS/NICHOLS SJC, 33608 ORTEGA HWY, SAN JUAN CAPISTRANO, CA 92675-2042 Laboratory Director: IRINA MARAMICA,MD,PHD,MBA, CLIA: 05D0643352